[{name:"Route 1",stops:["stop1Id","stop2Id","stop3Id","stop4Id"]},{name:"Route 2",stops:["stop4Id","stop3Id","stop2Id","stop1Id"]}]

db.collection.find({"$expr":{"$gt":[{"$indexOfArray":["$stops","stop2Id"]},{"$indexOfArray":["$stops","stop4Id"]}]}})